RELA is required for CD271 expression and stem-like characteristics in hypopharyngeal cancer [dataset 2]
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE212398 | GEO | 2022/10/26
REPOSITORIES: GEO
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Project description:To investigate the mechanisms of CD271 transcription, we analyzed the difference between sorted CD271-low and CD271 expression-recovered cells.
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Project description:Analyze and compare the gene expression profile of human bone marrow primary CD45-CD271+ and CD45-CD271- cells. The hypothesis was some genes were differentially expressed in these two populations. Results provided important information regarding the gene expression difference of these two cell populations.
2015-03-17 | GSE57927 | GEO
Project description:Background: Large-scale genomic analyses of patient cohorts have revealed extensive heterogeneity between individual tumors, contributing to treatment failure and drug resistance. In malignant melanoma, heterogeneity is thought to arise as a consequence of the differentiation of melanoma-initiating cells that are defined by cell-surface markers like CD271 or CD133. Results: Here we identified the nerve growth factor receptor (CD271) as a crucial determinant of melanoma cell tumorigenicity, stem-like properties, heterogeneity and plasticity. Stable shRNA mediated knock-down of CD271 in patient-derived melanoma cells abrogated their tumor-initiating and colony-forming capacity. A genome-wide expression profiling and gene-set enrichment analysis revealed novel connections of CD271 with melanoma-associated genes like CD133 and points to a neural crest stem cell (NCSC) signature lost upon CD271 knock-down. In a meta-analysis, we found CD271 linked to the neural crest specifier SOX10 and observed a shared set of 271 differentially regulated genes. To dissect the connection of CD271 and CD133 we analyzed 10 patient-derived melanoma-cell lines for cell-surface expression of both markers compared to established cell lines MeWo and A375. We found CD271+ cells in the majority of cell lines analyzed as well as in a set of 16 different patient-derived melanoma metastases. Strikingly, only 2/12 cell lines harbored a CD133+ sub-set that in addition comprised a fraction of cells of a CD271+/CD133+ phenotype. Those cells were found in the label-retaining fraction and in vitro deduced from CD271+ but not CD271 knock-down cells. Conclusions: Our present study provides a deeper insight into the regulation of melanoma cell properties and points CD271 out as a regulator of several melanoma-associated genes. Further, our data strongly suggest CD271 is a crucial determinant of stem-like properties of melanoma cells like colony-formation and tumorigenicity.
2013-11-19 | GSE52456 | GEO
Project description:Background: Large-scale genomic analyses of patient cohorts have revealed extensive heterogeneity between individual tumors, contributing to treatment failure and drug resistance. In malignant melanoma, heterogeneity is thought to arise as a consequence of the differentiation of melanoma-initiating cells that are defined by cell-surface markers like CD271 or CD133. Results: Here we identified the nerve growth factor receptor (CD271) as a crucial determinant of melanoma cell tumorigenicity, stem-like properties, heterogeneity and plasticity. Stable shRNA mediated knock-down of CD271 in patient-derived melanoma cells abrogated their tumor-initiating and colony-forming capacity. A genome-wide expression profiling and gene-set enrichment analysis revealed novel connections of CD271 with melanoma-associated genes like CD133 and points to a neural crest stem cell (NCSC) signature lost upon CD271 knock-down. In a meta-analysis, we found CD271 linked to the neural crest specifier SOX10 and observed a shared set of 271 differentially regulated genes. To dissect the connection of CD271 and CD133 we analyzed 10 patient-derived melanoma-cell lines for cell-surface expression of both markers compared to established cell lines MeWo and A375. We found CD271+ cells in the majority of cell lines analyzed as well as in a set of 16 different patient-derived melanoma metastases. Strikingly, only 2/12 cell lines harbored a CD133+ sub-set that in addition comprised a fraction of cells of a CD271+/CD133+ phenotype. Those cells were found in the label-retaining fraction and in vitro deduced from CD271+ but not CD271 knock-down cells. Conclusions: Our present study provides a deeper insight into the regulation of melanoma cell properties and points CD271 out as a regulator of several melanoma-associated genes. Further, our data strongly suggest CD271 is a crucial determinant of stem-like properties of melanoma cells like colony-formation and tumorigenicity. For knock-down of CD271 (NGFR), melanoma cells were transfected with 2 M-BM-5g of each shRNA plasmid; #2: 5M-bM-^@M-^Y-ACAACCTCATCCCTGTCTATT-3M-bM-^@M-^Y; #3: 5M-bM-^@M-^Y-CCCGAGCACATAGA CTCCTTT-3M-bM-^@M-^Y and #4: 5M-bM-^@M-^Y-CCGAGCACATAGACTCCTTTA-3M-bM-^@M-^Y or control shRNA (shCtl 5M-bM-^@M-^Y-GGAATCTCATTCGATGCATAC-3M-bM-^@M-^Y; all from Quiagen) using Lipofectamine2000 (Invitrogen). Cells were selected with puromycin (10M-BM-5g/ ml) over a period of two weeks. Whole genome expression profiling of CD271k.d. cells (shRNA#4) and shCtl. cells was performed with three biological replicates. Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization. Genes were termed significantly differentially expressed when the average detection p-value of at least one case was < 0.05 the ratio was outside the interval [0.75,1.33], one of the p-values from limma test, Student's t-test, Welch test and Wilcoxon test was < 0.05. At least one of the q-values corresponding to one of these tests < 0.05.
2013-11-19 | E-GEOD-52456 | biostudies-arrayexpress
Project description:The extensive heterogeneity both between and within the medulloblastoma (MB) subgroups underscores a critical need for variant-specific biomarkers and therapeutic strategies. We previously identified a role for the CD271/p75 neurotrophin receptor (p75NTR) in regulating stem/progenitor cells in the SHH MB subgroup. Here, we demonstrate the utility of CD271 as a novel diagnostic and prognostic marker for SHH MB using immunohistochemical analysis as well as transcriptome data across 763 primary tumors. Characterization of CD271+ and CD271- cells by RNA sequencing revealed that these two subpopulations are molecularly distinct, co-existing cellular subsets both in vitro and in vivo. MAPK/ERK signaling is upregulated in the CD271+ population and inhibiting this pathway reduced CD271 levels, stem/progenitor cell proliferation and cell survival as well as cell migration in vitro. Importantly, the MEK inhibitor selumetinib extends survival and reduces CD271 levels in vivo. Our study demonstrates the clinical utility of CD271 as both a diagnostic and prognostic tool for SHH MB tumors and reveals a novel role for MEK inhibitors in targeting CD271+ SHH MB cells.
2019-12-31 | GSE107701 | GEO
Project description:Differences in gene expression between unsorted adipose tissue-derived mesenchymal stem cells (AD-MSCs), and a specific subpopulation that has been selected for the expression of the surface marker CD271. It is believed that the selection of this specific subpopulation from the heterogeneous SVF will lead to mesenchymal stem cells with higher angiogenetic potential.
2021-01-27 | E-MTAB-8740 | biostudies-arrayexpress
Project description:Genome-wide expression profiling of stably NGFR transfected melanoma cells was used to identify genes driven by expression of the nerve growth factor receptor CD271 (NGFR). Stable overexpression of NGFR (CD271): Generation of cell lines stably overexpressing CD271 (NGFR), melanoma cells were transfected with 2 µg of a plasmid expressing GFP-tagged human NGFR (RG207966, OriGene) and selected with G418 (100-300 µg/ml, PAA) over a period of two weeks followed by sub-cloning or FACS. Gene expression profiling: Whole genome expression profiling of T20/02 and A375 cells (NGFR) and control cells (Mock or GFP) was performed with three biological replicates. Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization. Genes were termed significantly differentially expressed when the average detection p-value of at least one case was < 0.05 the ratio was outside the interval [0.75,1.33], one of the p-values from limma test, Student's t-test, Welch test and Wilcoxon test was < 0.05. At least one of the q-values corresponding to one of these tests < 0.05.
2016-02-23 | E-GEOD-78155 | biostudies-arrayexpress
Project description: Not available
| S-EPMC3633921 | biostudies-literature
Project description:Genome-wide expression profiling of stably NGFR transfected melanoma cells was used to identify genes driven by expression of the nerve growth factor receptor CD271 (NGFR).
2016-02-23 | GSE78155 | GEO